Amino acids also serve as precursors to form larger structures such as vitamins. For example, bacteria may assemble eight molecules of glutamic acid into a giant ring structure called a tetrapyrrole. Tetrapyrrole derivatives include essential cofactors of energy transduction and biosynthesis, such as chlorophylls, hemes of cytochromes and hemoglobin, and vitamin B12. Tetrapyrrole biosynthesis and its control by riboswitches are described in .
In addition to the standard amino acids used by ribosomes, there exist hundreds of different amino acids used by cells for functions such as the cross-bridges of peptidoglycan (discussed in ). Some of these are made by one-step modification of standard amino acids, such as epimerization (altering the chirality from to ) or halogenation with chlorine or fluorine. Others have complex carbon skeletons, including unsaturated bonds and three-membered rings. Both standard and nonstandard amino acids are used by actinomycetes to build secondary metabolites with antimicrobial activity. These secondary metabolites are called because their peptide backbone is constructed by an enzyme without ribosomes. Nonribosomal peptide antibiotics are synthesized by modular “assembly-line” enzymes, analogous to those that build polyketides. An example is vancomycin, the main antibiotic used against the lethal hospital-borne pathogen . Vancomycin biosynthesis is presented in .
Ammonia is toxic to cells. Transamination enables cells to store amine groups in nontoxic form, readily available for biosynthesis. The availability of multiple enzymes of transamination from different amino acids enables cells to quickly recycle existing resources into the amino acids most needed by the cell in a given environment. For example, if a sudden supply of glutamine appears, cells can immediately distribute its amines into all 20 amino acids.
Nitric oxide (NO) is a recently discovered mediator produced by mammalian cells. It plays a key role in neurotransmission, control of blood pressure, and cellular defense mechanisms. Nitric oxide synthases (NOSs) catalyze the oxidation of L-arginine to NO and L-citrulline. NOSs are unique enzymes in that they possess on the same polypeptidic chain a reductase domain and an oxygenase domain closely related to cytochrome P450s. NO and superoxide formation as well as NOS stability are finely regulated by Ca2+/calmodulin interactions, by the cofactor tetrahydrobiopterin, and by substrate availability. Strong interactions between the L-arginine-metabolizing enzymes are clearly demonstrated by competition between NOSs and arginases for L-arginine utilization, and by potent inhibition of arginase activity by Nω-hydroxy-L-arginine, an intermediate in the L-arginine to NO pathway.
The cellular levels of glutamate and glutamine act as indicators of nitrogen availability. When nitrogen is scarce, NtrC is phosphorylated to NtrC-P as we saw earlier in . Along with nitrogenase, NtrC-P up-regulates expression of glutamine synthetase (), as well as a high-affinity ammonia transporter, and transporters for organic sources of nitrogen such as amino acids, oligopeptides, and cell wall fragments containing amino sugars. All these molecules can be “scavenged” to obtain nitrogen for biosynthesis.
The carbon skeletons of amino acids arise from diverse intermediates of metabolism (see ). As in fatty acid biosynthesis, precursor molecules are channeled into amino acid biosynthesis by specialized cofactors and reducing energy carriers such as NADPH. Note that certain amino acids arise directly from key metabolic intermediates (for example, glutamate from 2-oxoglutarate), whereas others must be synthesized from preformed amino acids (for example, glutamine, proline, and arginine from glutamate). Some amino acids can arise from more than one source; for example, leucine and isoleucine can be made from succinate as well as from pyruvate.
Like fatty acid biosynthesis, synthesis of amino acids and nitrogenous bases requires the input of large amounts of reducing energy. These compounds pose additional challenges because of their unique and diversified forms, which cannot be made by the cyclic processes that generate molecules from repeating units. Synthesis of complex, asymmetrical molecules such as amino acids requires many different conversions, each mediated by a different enzyme. Nevertheless, some economy is gained by an arrangement of branched pathways in which early intermediates are utilized to form several products (). For example, oxaloacetate is converted to aspartate, which can be converted to four other amino acids.
Fragments of a meteorite that fell in Murchison, Australia, in 1969 were shown to contain the five fundamental amino acids of biosynthetic pathways (glutamate, aspartate, valine, alanine, and glycine).
It has been hypothesized that the amino acids arising in just one or two steps from central intermediates are more ancient in cell evolution than those requiring more complex pathways. Five of these “ancient” amino acids—glutamate, aspartate, valine, alanine, and glycine—are the same as those detected in meteorites, whose composition resembles that of prebiotic Earth (). These same five amino acids also appear in early-Earth simulation experiments in which methane, ammonia, and water are heated under reducing conditions and subjected to electrical discharge. Thus, we speculate that the first amino acids that early cells evolved to make were the same as those that arose spontaneously in the prebiotic chemistry of our planet.
A more subtle effect of evolution has been to adjust the amino acid composition of proteins based on the energetic cost of biosynthesis. Proteins that are secreted or that project outside the cell cannot be recycled; their amino acids are ultimately lost to the cell. Thus, secreted and externally projecting proteins have evolved to contain the “cheaper” amino acids—that is, the amino acids whose synthesis requires spending fewer molecules of ATP and NADPH. This effect can be seen in the diagram of a bacterial flagellum and its attached motor, which contains extracellular as well as cytoplasmic components, colored on a scale based on biosynthetic “expense” (). The external and secreted components favor less expensive amino acids, compared to the cytoplasmic components.
Unlike sugars and fatty acids, amino acids must assimilate another key ingredient: nitrogen. The NH4+ produced by N2 fixation or by nitrate reduction is the key source of nitrogen for biosynthesis. But NH4+ always exists in equilibrium with NH3, which is toxic to cells. Moreover, NH3 travels freely through membranes, making it difficult to store NH4+ within a cell. Deprotonation to NH3 increases as pH rises; by pH 9.2, deprotonation reaches 50%. Even at neutral pH, a very small equilibrium concentration of NH3 can drain NH4+ out of the cell. Thus, cells avoid storing high levels of NH4+; instead, the fixed nitrogen is incorporated immediately into organic products.
Both glutamate and glutamine contribute an amine, as well as their carbon skeletons, to the synthesis of other amino acids in the biosynthetic “tree.” The transfer of ammonia between two metabolites such as glutamate and glutamine is called . Many other pairs of amino acids and metabolic intermediates undergo transamination. For example, glutamate transfers NH3 to oxaloacetate, making aspartate and 2-oxoglutarate; the reaction can also be reversed. In another example, valine transfers an amine group to pyruvate, generating alanine and 2-ketoisovalerate.